The Philippines is one of the more expensive Southeast Asian countries for domestic transportation, simply because exploring an archipelago of over 7,000 islands requires traversing a lot of waterways.
Boat travel is the most affordable mode of transport if the destination is in close proximity and you need to travel between islands. If you need to cover longer distances then you will need to fly.
Most tourists to the Philippines find air travel necessary at some point during their visit. Many visitors begin and end their trip in Luzon and/or Cebu, due to affordable international flights in and out of Manila and Cebu City.
The remote location of the country means that even the shortest international flights (to Kuala Lumpur in Malaysia) are generally more expensive than international flights between other Southeast Asian countries, and this also discourages visa runs.
By car and bus
Unique to the Philippines and one of their cultural symbols is the jeepney, which is really a hybrid between a jeep and a bus, and generally packed to maximum capacity. Cheap and an integral facet of the local experience, jeepneys are a good low cost way of getting around.
More commonly used than taxis in the Philippines are trikes. Unlike jeepneys that have set routes, a trike will take you wherever you need to go so long as you can negotiate a fair price.